+Open data
-Basic information
Entry | Database: PDB / ID: 5foo | ||||||
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Title | 6-phospho-beta-glucosidase | ||||||
Components | 6-PHOSPHO-BETA-D GLYCOSIDASE | ||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / CYCLOPHELLITOL / GLUCOSE 6-PHOSPHATE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOCOCCUS PYOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Jin, Y. / Kwan, D.H. / Withers, S.G. / Davies, G.J. | ||||||
Citation | Journal: FEBS Lett. / Year: 2016 Title: Chemoenzymatic Synthesis of 6-Phospho-Cyclophellitol as a Novel Probe of 6-Phospho-Beta-Glucosidases. Authors: Kwan, D.H. / Jin, Y. / Jiang, J. / Chen, H. / Kotzler, M.P. / Overkleeft, H.S. / Davies, G.J. / Withers, S.G. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "FB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5foo.cif.gz | 575.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5foo.ent.gz | 476.2 KB | Display | PDB format |
PDBx/mmJSON format | 5foo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/5foo ftp://data.pdbj.org/pub/pdb/validation_reports/fo/5foo | HTTPS FTP |
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-Related structure data
Related structure data | 4b3kS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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6 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 55152.699 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: M1 GAS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q99YP9, beta-glucosidase, 6-phospho-beta-glucosidase |
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-Non-polymers , 6 types, 1016 molecules
#2: Chemical | ChemComp-JAZ / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PO4 / #5: Chemical | #6: Chemical | ChemComp-TRS / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.7 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.33 MM SPY1599 WAS REACTED WITH 4.2 MM 6-PHOSPHO-CYCLOPHELLITOL EPOXIDE IN THE BUFFER OF 50 MM HEPES AND 150 MM NACL, PH 7.0, BEFORE BEING MIXED WITH THE SAME VOLUME OF BUFFER OF 0.1 M BIS ...Details: 0.33 MM SPY1599 WAS REACTED WITH 4.2 MM 6-PHOSPHO-CYCLOPHELLITOL EPOXIDE IN THE BUFFER OF 50 MM HEPES AND 150 MM NACL, PH 7.0, BEFORE BEING MIXED WITH THE SAME VOLUME OF BUFFER OF 0.1 M BIS TRIS PROPANE PH7.5, 20% PEG 3350 AND 0.15 M NABR |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→49.47 Å / Num. obs: 205534 / % possible obs: 99.9 % / Observed criterion σ(I): 1.9 / Redundancy: 4.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4B3K Resolution: 2.1→158.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.019 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.306 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→158.4 Å
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